Re: [galaxy-dev] ToolShed test failure: NotFound: cannot find 'ucsc_display_sites' while searching for 'APP.config.ucsc_display_sites'

[Peter Cock]

On Wed, Sep 10, 2014 at 7:55 PM, Nate Coraor n...@bx.psu.edu wrote:
 Hi Peter,

 This was due to a bug I introduced last week, which I've just fixed in
 d1f6d05. Sorry for the trouble.

 --nate

Thanks - I'll check back in a day or two once the tests have
run again.

Peter
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Re: [galaxy-dev] ToolShed test failure: NotFound: cannot find 'ucsc_display_sites' while searching for 'APP.config.ucsc_display_sites'

[Nate Coraor]

Hi Peter,

This was due to a bug I introduced last week, which I've just fixed
in d1f6d05. Sorry for the trouble.

--nate

On Tue, Sep 9, 2014 at 9:50 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:

 Hi all,

 I'm wondering why my samtools_depad repository tests have
 failed, and since I have not changed this recently presume this
 is due to a Galaxy change or general TestToolShed problem
 not specific to my tool:

 https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad

 Tests that failed
 Tool id: samtools_depad
 Tool version: samtools_depad
 Test: test_tool_00
 (
 functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/samtools_depad/samtools_depad/0.0.1
 )
 Stderr:
 Traceback:
 Traceback (most recent call last):
   File
 /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py,
 line 114, in test_tool
 self.do_it( td )
   File
 /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py,
 line 35, in do_it
 self._verify_outputs( testdef, test_history, shed_tool_id,
 data_list, galaxy_interactor )
   File
 /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py,
 line 75, in _verify_outputs
 galaxy_interactor.verify_output( history, output_data,
 output_testdef=output_testdef, shed_tool_id=shed_tool_id,
 maxseconds=maxseconds )
   File
 /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py,
 line 82, in verify_output
 self._verify_metadata( history_id, hid, attributes )
   File
 /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py,
 line 103, in _verify_metadata
 raise Exception( msg )
 Exception: Dataset metadata verification for [file_ext] failed,
 expected [bam] but found [None].
 Traceback (most recent call last):
   File
 /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/web/framework/decorators.py,
 line 243, in decorator
 rval = func( self, trans, *args, **kwargs)
   File
 /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/webapps/galaxy/api/history_contents.py,
 line 188, in show
 return self.__show_dataset( trans, id, **kwd )
   File
 /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/webapps/galaxy/api/history_contents.py,
 line 214, in __show_dataset
 hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda )
   File
 /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/web/base/controller.py,
 line 855, in get_display_apps
 for display_app in hda.get_display_applications( trans ).itervalues():
   File
 /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/model/__init__.py,
 line 1754, in get_display_applications
 return self.datatype.get_display_applications_by_dataset( self, trans )
   File
 /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/datatypes/data.py,
 line 445, in get_display_applications_by_dataset
 value = value.filter_by_dataset( dataset, trans )
   File
 /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/datatypes/display_applications/application.py,
 line 200, in filter_by_dataset
 if link_value.filter_by_dataset( data, trans ):
   File
 /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/datatypes/display_applications/application.py,
 line 78, in filter_by_dataset
 if fill_template( filter_elem.text, context = context ) !=
 filter_elem.get( 'value', 'True' ):
   File
 /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/util/template.py,
 line 9, in fill_template
 return str( Template( source=template_text, searchList=[context] ) )
   File
 /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py,
 line 1004, in __str__
 return getattr(self, mainMethName)()
   File cheetah_DynamicallyCompiledCheetahTemplate_1410263883_33_43576.py,
 line 82, in respond
 NotFound: cannot find 'ucsc_display_sites' while searching for
 'APP.config.ucsc_display_sites'
 requests.packages.urllib3.connectionpool: DEBUG: GET

 /api/histories/993bad2fe35335db/contents/7fbe67cfae825002?key=edc04240db9605fb7edc7bab44d3404c
 HTTP/1.1 500 None
 requests.packages.urllib3.connectionpool: INFO: Starting new HTTP
 connection (1): 127.0.0.1
 requests.packages.urllib3.connectionpool: DEBUG: GET

 /api/histories/993bad2fe35335db/contents/7fbe67cfae825002/provenance?key=edc04240db9605fb7edc7bab44d3404c
 HTTP/1.1 200 None